viewKegg {CompGO} | R Documentation |
viewKegg uses pathview to compare the gene lists visually by KEGG pathway. You can either supply a pathway id or the function will pick the most differentially enriched pathway between the two inputs. As functional annotation charts don't have differential gene expression information, a boolean scale is used - genes in the pathway are coloured green if from setA, yellow if from both, and red if from setB. We recommend you supply a working directory, as pathview will download an XML and PNG file as well as output an additional PNG of the pathway.
viewKegg(setA, setB, keggTerm = NULL, species = NULL, workingDir = NULL, sortByCount = FALSE, ...)
setA |
FunctionalAnnotationChart to compare |
setB |
FunctionalAnnotationChart to compare |
keggTerm |
If a specific KEGG pathway is of interest, input the name here; otherwise, the most differentially expressed pathway will be used. |
species |
The program can usually figure out the species from the KEGG terms, but if it can't, supply the species ID here. From pathview vignette, run 'data(bods); bods' to find species codes. |
workingDir |
The directory to output into. Recommended, since pathview will put a few different files there each time. |
sortByCount |
Set TRUE if you want the function to automatically choose the pathway with the most number of genes |
... |
Arguments to be passed to pathview |
Output from pathview: a list of 2, plot.data.gene and plot.data.cpd
## Not run: # Since this function requires writing to a directory, it won't be run here data(funChart1) data(funChart2) viewKegg(funChart1, funChart2) ## End(Not run)